The human Y chromosome is distinguished from all other nuclear chromosomes by four characteristics: the absence of recombination, its presence in males only, its common ancestry and persistent meiotic relationship with the X chromosome, and the tendency of its genes to degenerate during evolution (J. J. Bull, Evolution of Sex Determining Mechanisms (Benjamin Cummings, Menlo Park, Calif., 1983); J. A. Graves, Annu. Rev. Genet. 30:233 (1996); B. Charlesworth, Curr. Biol. 6:149 (1996); W. R. Rice, BioScience, 46, 331 (1996)). To be precise, these distinctive characteristics apply only to the non-recombining portion or region of the Y chromosome (NRY), which comprises 95% of the human Y chromosome. The remaining 5% of the chromosome is composed of two pseudoautosomal regions that maintain sequence identity with the X chromosome by meiotic recombination (H. J. Cooke et al., Nature 317:687 (1985); M. C. Simmler et al., Nature 317:692 (1985); D. Freije et al., Science 258:1784 (1992); G. A. Rappold, Hum. Genet. 92:315 (1993)). Given the NRY's peculiar characteristics, one might expect its gene content to be idiosyncratic. Since discovery of the Y chromosome in 1923, its gene content has been the subject of speculation. By the middle of this century, while studies of human pedigrees had identified many traits exhibiting autosomal or X-linked inheritance, no convincing cases of Y-linked inheritance could be found (T. S. Painter, J. Exp. Zool. (1923); C. Stern, Am. J. Hum. Genet. 9:147 (1957)). As a result, consensus began to emerge that the Y chromosome carried few, if any, genes. In 1959, reports of XO females and XXY males established the existence of a sex-determining gene on the human Y chromosome (P. A. Jacobs et al. Nature 183:302 (1959); C. E. Ford et al., Lancet, i:711 (1959)), but this was perceived as a special case on a generally desolate chromosome. Opionions began to change only during the past decade, when eight NRY transcription units (or families of closely related transcription units) were identified, most during regionally focused, positional closing experiments (D. C. Page et al., Cell 51:1091 (1987); A. H. Sinclair et al., Nature 346:240-244 (1990); J. Arnemann et al., Genomics 11: 108 (1991); E. C. Salido et al., Am. J. Hum. Genet. 50:303 (1992); E. M. Fisher et al., Cell 63:1205 (1990); K. Ma et al., Cell 75:1287 (1993); A. I. Agulnik et al., Hum. Mol. Genet. 3:879 (1994); R. Reijo et al., Nat. Genet. 10:383 (1995)). It was not known if there were more genes in the NRY.